Dan,
Thanks for the followup. That’s wired. I use R 3.0.0 here. It is different from
R-3.1.0, but I don’t think it would make such a difference in generating the
error below:
Error in bods[idx, "id.type"] : subscript out of bounds
I run the exact same build command on my local machine (as below), I got the
same error indeed:
R CMD build --keep-empty-dirs --no-resave-data gage
But if I install gage package first, then then create vignettes manually,
everything is fine.
sudo R CMD INSTALL gage
cd gage/vignettes/
R CMD Sweave gage.Rnw
R CMD texi2dvi -p gage.tex
I am not sure, why there is such a difference. Do you have any idea on this?
I suspected that bods data file (bods.rda in the data directory) was not
updated or have some problem somehow. Below is the problematic code chunk in
the go.gset.R file:
…
idx=which(bods[,"species"] == species)
if(length(idx)!=1) stop("bad species value")
pkg.name = bods[idx, "package"]
id.type=toupper(bods[idx, "id.type"])
…
I tried to insert the following two lines:
print(head(bods))
print(idx)
before the last line above and rerun rerun: R CMD build --keep-empty-dirs
--no-resave-data gage
The error still exists, but I don’t see the printed out results from the newly
added lines, hence not able to figure out what happened there.
so far, I can think of anything wrong with gage package. because the manual
install and vignette creating worked. The only problem I am sure is that R CMD
build --keep-empty-dirs --no-resave-data behave differently from the manual
process. Could you help to check into the problem here? Thank you! I am cc’ing
the devel list see if other people got the same problem.
Weijun
--------------------------------------------
On Fri, 4/4/14, Dan Tenenbaum <dtene...@fhcrc.org> wrote:
Subject: Re: unexpected build and check error
Date: Friday, April 4, 2014, 12:24 PM
Hi Weijun,
gage is still broken today:
http://www.bioconductor.org/checkResults/2.14/bioc-LATEST/gage/zin2-buildsrc.html
It seems to be using the latest versions:
> packageVersion("gage")
[1] ‘2.13.5’
> packageVersion("pathview")
[1] ‘1.3.4’
So maybe the cause of the problem is different? Have you
tried using the most recent R? (R-3.1.0 RC)?
Dan
----- Original Message -----
> From: "Dan Tenenbaum" <dtene...@fhcrc.org>
> Sent: Thursday, April 3, 2014 10:24:10 AM
> Subject: Re: unexpected build and check error
>
> No, I think it will be ok tomorrow. If not I'll make
sure it gets
> fixed.
> Thanks,
> Dan
>
>
> ----- Original Message -----
> > To: "Dan Tenenbaum" <dtene...@fhcrc.org>
> > Sent: Thursday, April 3, 2014 10:19:16 AM
> > Subject: unexpected build and check error
> >
> > Dear Dan,
> > I got the following error in the bioc 2.14 build
report:
> > http://bioconductor.org/checkResults/devel/bioc-LATEST/gage/zin2-buildsrc.html
> >
> > Error: processing vignette 'gage.Rnw' failed with
diagnostics:
> > chunk 12 (label = go.gsets)
> > Error in bods[idx, "id.type"] : subscript out of
bounds
> > Execution halted
> >
> > I believe this is due to the loading of the old
pathview package at
> > that time, which carries a copy of obsolete bods
hence interfered
> > the build/check. But since pathview and gage was
updated at the
> > same
> > time. This error will be gone in the next
building/checking cycle.
> > My local copy does get through the
building/checking free of error.
> > Shall we do something given that the today is
“Deadline for
> > packages
> > passing R CMD build and check without warning”?
thanks!
> > Weijun
> >
> >
>
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